Selection-driven trait loss in independently evolved cavefish populations

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: May 3, 2023

Abstract Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found phenotypic convergence due to parallel genetic changes. This suggests substantial role for constraint and determinism evolution indicates certain mutations are more likely contribute evolution. Here we use whole genome resequencing the Mexican tetra, Astyanax mexicanus , investigate how selection has shaped repeated of both trait loss enhancement across independent cavefish lineages. We show on standing variation de novo substantially adaptation. Our findings provide empirical support hypothesis genes with larger mutational targets substrate indicate features cave environment may impact rate at which occur.

Language: Английский

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A vertebrate adaptive radiation is assembled from an ancient and disjunct spatiotemporal landscape

Proceedings of the National Academy of Sciences, Journal Year: 2021, Volume and Issue: 118(20)

Published: May 14, 2021

To investigate the origins and stages of vertebrate adaptive radiation, we reconstructed spatial temporal histories alleles underlying major phenotypic axes diversification from genomes 202 Caribbean pupfishes. On a single Bahamian island, ancient standing variation disjunct geographic sources was reassembled into new combinations under strong directional selection for adaptation to novel trophic niches scale-eating molluscivory. We found evidence two longstanding hypotheses radiation: hybrid swarm adaptation. Using combination population genomics, transcriptomics, genome-wide association mapping, demonstrate that this microendemic radiation specialists on San Salvador Island, Bahamas experienced twice as much introgression generalist populations neighboring islands divergence occurred in stages. First, regulatory genes associated with feeding behavior (

Language: Английский

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Rapid adaptive radiation of Darwin’s finches depends on ancestral genetic modules

Science Advances, Journal Year: 2022, Volume and Issue: 8(27)

Published: July 8, 2022

Recent adaptive radiations are models for investigating mechanisms contributing to the evolution of biodiversity. An unresolved question is relative importance new mutations, ancestral variants, and introgressive hybridization phenotypic speciation. Here, we address this issue using Darwin’s finches investigate genomic architecture underlying their diversity. Admixture mapping beak body size in small, medium, large ground revealed 28 loci showing strong genetic differentiation. These represent haplotype blocks with origins predating speciation events during finch radiation. Genes expressed developing overrepresented these regions. Ancestral haplotypes constitute modules selection act as key determinants unusual diversity finches. Such can be critical how species adapt environmental variability change.

Language: Английский

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Genomic architecture of adaptive radiation and hybridization in Alpine whitefish

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: Aug. 2, 2022

Adaptive radiations represent some of the most remarkable explosions diversification across tree life. However, constraints to rapid and how they are sometimes overcome, particularly relative roles genetic architecture hybridization, remain unclear. Here, we address these questions in Alpine whitefish radiation, using a whole-genome dataset that includes multiple individuals each 22 species belonging six ecologically distinct ecomorph classes several lake-systems. We reveal repeated ecological morphological along common environmental axis is associated with both genome-wide allele frequency shifts specific, larger effect, locus, gene edar. Additionally, highlight possible role introgression between from different lake-systems facilitating evolution persistence unique trait combinations ecology. These results importance genome secondary contact hybridization fuelling adaptive radiation.

Language: Английский

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The Role of Hybridization in Species Formation and Persistence

Cold Spring Harbor Perspectives in Biology, Journal Year: 2024, Volume and Issue: 16(12), P. a041445 - a041445

Published: March 4, 2024

Joshua V. Peñalba1, Anna Runemark2, Joana I. Meier3,4, Pooja Singh5,6, Guinevere O.U. Wogan7, Rosa Sánchez-Guillén8, James Mallet9, Sina J. Rometsch10,11, Mitra Menon12, Ole Seehausen5,6, Jonna Kulmuni13,14,16 and Ricardo Pereira15,16 1Museum für Naturkunde, Leibniz Institute for Evolution Biodiversity Science, Center Integrative Discovery, 10115 Berlin, Germany 2Department of Biology, Lund University, 22632 Lund, Sweden 3Tree Life, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, United Kingdom 4Department Zoology, University Cambridge, CB2 3EJ, 5Department Aquatic Ecology, Ecology Evolution, Bern, 3012 Switzerland 6Center & Biogeochemistry, Swiss Federal Science Technology (EAWAG), CH-8600 Kastanienbaum, 7Department Oklahoma State Stillwater, 74078, USA 8Red de Biología Evolutiva, INECOL, Xalapa, Veracruz, CP 91073, Mexico 9Organismal Evolutionary Harvard Massachusetts 02138, 10Department Yale New Haven, Connecticut 06511, 11Yale Biospheric Studies, 12Department California Davis, 95616, 13Department Population Ecosystem Dynamics, Amsterdam, 1098 XH The Netherlands 14Organismal Biology Research Programme, Helsinki, Biocenter 3, Finland 15Department Museum Natural History Stuttgart, Stuttgart 70191, Correspondence: ricardojn.pereira{at}gmail.com ↵16 These authors contributed equally to this work.

Language: Английский

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Linking human impacts to community processes in terrestrial and freshwater ecosystems

Ecology Letters, Journal Year: 2022, Volume and Issue: 26(2), P. 203 - 218

Published: Dec. 22, 2022

Human impacts such as habitat loss, climate change and biological invasions are radically altering biodiversity, with greater effects projected into the future. Evidence suggests human may differ substantially between terrestrial freshwater ecosystems, but reasons for these differences poorly understood. We propose an integrative approach to explain by linking four fundamental processes that structure communities: dispersal, speciation, species-level selection ecological drift. Our goal is provide process-based insights why impacts, responses across ecosystem types using a mechanistic, eco-evolutionary comparative framework. To enable insights, we review synthesise (i) how influence diversity dynamics in versus communities, specifically whether relative importance of each process differs among (ii) pathways which can produce divergent due strength ecosystems identify. Finally, highlight research gaps next steps, discuss this new conservation. By focusing on shape aim mechanistically link ongoing future changes ecosystems.

Language: Английский

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Toward the integration of speciation research

Evolutionary Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: 3(1)

Published: Jan. 1, 2024

Abstract Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long complex history. While relevant to one another, specific goals activities speciation researchers are highly diverse, scattered across collection different perspectives. Thus, our will benefit from efforts bridge findings diverse people who do work. In this paper, we outline two ways integrating research: (i) integration, through bringing together ideas, data, approaches; (ii) social by creating for participate in process. We then discuss five challenges integration: multidisciplinary nature research, language speciation; (iii) bias toward certain study systems; (iv) working scales; (v) inconsistent measures reporting standards. provide practical steps that individuals groups can take help overcome these challenges, argue integration is team effort which all have role play.

Language: Английский

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Biogeography of Greater Antillean freshwater fishes, with a review of competing hypotheses

Biological reviews/Biological reviews of the Cambridge Philosophical Society, Journal Year: 2024, Volume and Issue: 99(3), P. 901 - 927

Published: Jan. 11, 2024

ABSTRACT In biogeography, vicariance and long‐distance dispersal are often characterised as competing scenarios. However, they related concepts, both relying on collective geological, ecological, phylogenetic evidence. This is illustrated by freshwater fishes, which may immigrate to islands either when connections temporarily present later severed (vicariance), or unusual means ocean gaps crossed (long‐distance dispersal). Marine barriers have a strong filtering effect limiting immigrants those most capable of oceanic dispersal. The roles debated for fishes the Greater Antilles. We review three active hypotheses [Cretaceous vicariance, Antilles–Aves Ridge (GAARlandia), dispersal] propose be an appropriate model due limited support fish use landspans. Antillean six potential source bioregions (defined from faunal similarity): Northern Gulf México, Western Maya Terrane, Chortís Block, Eastern Panamá, South America. Faunas Antilles composed taxa immigrating many these bioregions, but there compositional disharmony between island mainland faunas (>90% species cyprinodontiforms, compared <10% in México America, ≤50% elsewhere), consistent with hypothesis Ancestral‐area reconstruction analysis indicates were 16 17 immigration events over last 51 million years, 14 15 cyprinodontiforms. Published divergence estimates evidence available each event suggests occurred at different times pathways, possibly rafts vegetation discharged rivers washed sea during storms. If so, currents likely provide critical pathways flowing one landmass another. On other hand, create perpendicularly landmasses. addition high salinity tolerance, cyprinodontiforms collectively display variety adaptations that could enhance their ability live (small body size, viviparity, low metabolism, amphibiousness, diapause, self‐fertilisation). These also helped establish populations after arrival persist long term thereafter. Cichlids used pseudo bridge (Nicaragua Rise) reach Gars (Lepisosteidae) Straits Florida Cuba, relatively short crossing not barrier gene flow several cyprinodontiform immigrants. Indeed, widespread distributions Quaternary migrants ( Cyprinodon , Gambusia Kryptolebias ), within among neighbouring imply necessarily inhibitory well‐adapted species, even though it appears virtually impossible all fishes.

Language: Английский

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From microcosm to macrocosm: adaptive radiation of Darwin’s finches

Evolutionary Journal of the Linnean Society, Journal Year: 2024, Volume and Issue: 3(1)

Published: Jan. 1, 2024

Abstract In this Perspective we show the value of studying living organisms in field to understand their history. Darwin’s finches are an iconic example early stages speciation a young adaptive radiation that produced 18 species little more than million years. The question they pose is how and why so many originated diversified rapidly. A long-term study four on small island Daphne Major, combined with genomic investigations, provide some answers terms extrinsic intrinsic factors. Beak size shape, as well body size, key heritable features involved both ecological reproductive isolation, evolution by natural selection was caused competitor during prolonged droughts. Introgressive hybridization related rare but recurring, apparently widespread, increases genetic variation, does not incur fitness cost. Hybridization can produce new species. We use phylogeny based whole genome sequences infer morphological transitions radiation. Several lines evidence indicate missing from phase due extinction. Combining these results, re-cast classical allopatry-then-sympatry theory competition-selection-hybridization process generates diversity

Language: Английский

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Parallel evolution of integrated craniofacial traits in trophic specialist pupfishes

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(7)

Published: July 1, 2024

Abstract Populations may adapt to similar environments via parallel or non‐parallel genetic changes, but the frequency of these alternative mechanisms and underlying contributing factors are still poorly understood outside model systems. We used QTL mapping investigate basis highly divergent craniofacial traits between scale‐eater ( Cyprinodon desquamator ) molluscivore C. brontotheroides pupfish adapting two different hypersaline lake on San Salvador Island, Bahamas. lab‐reared F2 x intercrosses from populations, estimated linkage maps, scanned for significant 29 skeletal traits, female mate preference, sex. compared location lakes quantify changes. detected six in at least one lake. However, nearly all shared loci were associated with a trait within each Therefore, our estimate evolution architecture could range out identical (low parallelism) five integrated (high parallelism). suggest that pleiotropy integration can affect estimates evolution, particularly rapid radiations. also observed increased adaptive introgression regions, suggesting gene flow contributed evolution. Overall, results same genomic regions contribute adaptation across suites rather than specific highlight need more expansive definition

Language: Английский

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